Variant report

Variant	rs10962648
Chromosome Location	chr9:16868958-16868959
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10962638	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10962642	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10962645	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10962647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10962649	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10962652	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10962653	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10962656	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10962658	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10962659	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11788047	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11789875	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11792249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12379687	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62541877	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62541878	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62541879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62541920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62541922	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62541923	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62541926	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62543561	0.83[AFR][1000 genomes]
rs62543578	0.83[AFR][1000 genomes]
rs62543579	0.83[AFR][1000 genomes]
rs62543581	0.83[AFR][1000 genomes]
rs62543582	0.83[AFR][1000 genomes]
rs62543583	0.83[AFR][1000 genomes]
rs62543584	0.83[AFR][1000 genomes]
rs62543585	0.83[AFR][1000 genomes]
rs72713890	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892651	chr9:16816755-16869240	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv892652	chr9:16843128-16958312	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv892653	chr9:16848790-16895610	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	nsv1018615	chr9:16865804-16960970	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv540074	chr9:16865804-16960970	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16864800-16869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16864800-16869400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:16865000-16869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:16865000-16869400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr9:16865000-16872000	Active TSS	Stomach Smooth Muscle	stomach
6	chr9:16866400-16871800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:16866600-16869600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:16866600-16872200	Active TSS	NHLF	lung
9	chr9:16866800-16872000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr9:16867400-16870200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:16867600-16869000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:16867600-16869200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:16867600-16869200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr9:16867600-16869400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:16867600-16871600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:16867600-16872200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:16867600-16872200	Active TSS	Colon Smooth Muscle	Colon
18	chr9:16867600-16872400	Active TSS	Ovary	ovary
19	chr9:16867800-16869000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
20	chr9:16867800-16869800	Flanking Active TSS	NH-A	brain
21	chr9:16867800-16869800	Flanking Active TSS	Osteobl	bone
22	chr9:16867800-16871200	Active TSS	Fetal Stomach	stomach
23	chr9:16868000-16869000	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr9:16868000-16869000	Enhancers	Hela-S3	cervix
25	chr9:16868000-16872200	Active TSS	Right Atrium	heart
26	chr9:16868000-16872200	Active TSS	HSMM	muscle
27	chr9:16868200-16869000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr9:16868200-16869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:16868200-16869200	Weak transcription	Placenta	Placenta
30	chr9:16868200-16869400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:16868200-16869600	Enhancers	Psoas Muscle	Psoas
32	chr9:16868200-16872000	Active TSS	HSMMtube	muscle
33	chr9:16868400-16869000	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:16868400-16869200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:16868400-16869200	Enhancers	NHEK	skin
36	chr9:16868400-16869400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr9:16868400-16869400	Enhancers	A549	lung
38	chr9:16868400-16872400	Active TSS	Rectal Smooth Muscle	rectum
39	chr9:16868600-16869000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:16868600-16869000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
41	chr9:16868600-16869000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:16868600-16869000	Enhancers	HUVEC	blood vessel
43	chr9:16868600-16869400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
44	chr9:16868600-16869400	Flanking Active TSS	NHDF-Ad	bronchial
45	chr9:16868600-16869600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
46	chr9:16868800-16869000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
47	chr9:16868800-16869000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr9:16868800-16869000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
49	chr9:16868800-16869000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
50	chr9:16868800-16869000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell

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